DrImpute: Imputing dropout events in single cell RNA sequencing data

Abstract

The single cell RNA sequencing (scRNA-seq) technique began a new era by allowing the observation of gene expression at the single cell level. However, there is also a large amount of technical and biological noise. Because of the low number of RNA transcriptomes and the stochastic nature of the gene expression pattern, there is a high chance of missing nonzero entries as zero, which are called dropout events. However, many statistical methods used for analyzing scRNA-seq data in cell type identification, visualization, and lineage reconstruction do not model for dropout events. We have developed DrImpute to impute dropout events, and it improves many of the statistical tools used for scRNA-seq analysis that do not account for dropout events. Our numerical studies with real data demonstrate the promising performance of the proposed method, which has been implemented in R.